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.\" ========================================================================
.\"
.IX Title "Report 3pm"
.TH Report 3pm "2014-08-15" "perl v5.20.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Zerg::Report \- get attributes from a BLAST file in a data structure
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Zerg::Report;
\&  
\&  my $zerg_report = new Zerg::Report("output.blastn");
\&  
\&  while($r=$zerg_report\->getReport())
\&  { 
\&    foreach my $hit (@{$r\->{hits}})
\&    {
\&      foreach my $hsp (@{$hit\->{hsps}})
\&      {
\&        print "$r\->{query_name} $hit\->{subject_name} $hsp\->{score_bits}\en";
\&      }
\&    }
\&  }
\&
\&  $zerg_report\->closeFile();
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 4
\&  Zerg::Report uses Zerg to parse a file \- or STDIN if file is not given \-
\&  containing one or multiple BLAST reports and, for each report, stores
\&  the obtained fields in a data structure made of arrays and hashes.
\&  Please consult the Zerg man page to see which fields are extracted.
\&
\&  The method getReport() reads a BLAST report from the input file and
\&  returns a reference to a data structure like the one in the example
\&  below. When no report is found, it returns undef. It dies from
\&  syntax errors in BLAST reports with a stack backtrace.
\&
\&  Example of a data structure returned by getReport():
\&  
\&  $r = {
\&          \*(Aqquery_name\*(Aq => \*(AqME1\-0081T\-R227\-B12\-U.G\*(Aq,
\&          \*(Aqblast_version\*(Aq => \*(AqBLASTX 1.3.6 [2002\-03\-05]\*(Aq,
\&          \*(Aqbyte_offset\*(Aq => 4981,
\&          \*(Aqquery_length\*(Aq => \*(Aq444\*(Aq,
\&          \*(Aqquery_annotation\*(Aq => \*(Aq\*(Aq
\&          \*(Aqround_begins\*(Aq => [ 0, 129, 201 ], # indicates the first hit in each round of iterated blast
\&          \*(Aqhits\*(Aq => [
\&                      {
\&                        \*(Aqsubject_annotation\*(Aq => \*(Aq(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD\-e]\*(Aq,
\&                        \*(Aqhsps\*(Aq => [
\&                                    {
\&                                      \*(Aqquery_end\*(Aq => \*(Aq82\*(Aq,
\&                                      \*(Aqsubject_ali\*(Aq => \*(AqASELEIFAALIECEA\-GSTDYDGMLAVASVVMNRVNHRYYPDTITGVIYQSGQFSPVASGKLDKVLKRGIKSSCLEVAKDA\*(Aq,
\&                                      \*(Aqquery_ali\*(Aq => \*(AqDAQTRKLAAIAYGEASGANDANEIGGIAWAVANRARAWGGK\-TVDGLLAADPNYTYAVKDG\-NQRYAKLMKATEAAIAADP\*(Aq,
\&                                      \*(Aqsubject_end\*(Aq => \*(Aq328\*(Aq,
\&                                      \*(Aqidentities\*(Aq => \*(Aq15\*(Aq,
\&                                      \*(Aqscore\*(Aq => \*(Aq87\*(Aq,
\&                                      \*(Aqpercent_positives\*(Aq => \*(Aq41\*(Aq,
\&                                      \*(Aqgaps\*(Aq => \*(Aq3\*(Aq,
\&                                      \*(Aqscore_bits\*(Aq => \*(Aq37.9\*(Aq,
\&                                      \*(Aqalignment_length\*(Aq => \*(Aq81\*(Aq,
\&                                      \*(Aqevalue\*(Aq => \*(Aq0.40\*(Aq,
\&                                      \*(Aqpercent_identities\*(Aq => \*(Aq18\*(Aq,
\&                                      \*(Aqpositives\*(Aq => \*(Aq34\*(Aq,
\&                                      \*(Aqquery_start\*(Aq => \*(Aq4\*(Aq,
\&                                      \*(Aqsubject_start\*(Aq => \*(Aq249\*(Aq
\&                                    }
\&                                  ],
\&                        \*(Aqsubject_length\*(Aq => \*(Aq880\*(Aq,
\&                        \*(Aqsubject_name\*(Aq => \*(Aqgi|16802882|ref|NP_464367.1|\*(Aq
\&                      },
\&                    ],
\&        };
.Ve
.SH "AUTHORS"
.IX Header "AUTHORS"
Apua\*~ Paquola <apua@iq.usp.br>, Abimael Machado <abimael@iq.usp.br> IQ-USP Bioinformatics Lab
.PP
Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Zerg
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 287:" 4
.IX Item "Around line 287:"
Non-ASCII character seen before =encoding in 'Apua\*~'. Assuming \s-1ISO8859\-1\s0